Here's another tip from Milan Jajal, this time on Operations Manager 2007:
Issue: Custom groups used in a Distributed Application may disappeared from the Groups list in the Authoring pane.
Note: Even though the custom group disappeared from the Groups list, if you do scoping on rules or monitors list, the group is listed if you select view all targets. That means the group is not getting deleted. It's actually still present in the database but its disappearing from the Groups List view.
This applies to System Center Operations Manager 2007 RTM or Service Pack 1 (SP1).
Cause: This is a known issue. Microsoft is aware of the issue and working on a solution. If you include any top level group (custom or built-in) in a distributed application then it may disappear from the Groups List.
Resolution: There are 2 possible workarounds for this issue:
1. Do not use Groups in Distributed Applications.
Since it is understood that this may not be a good option in many cases, the second workaround can also be used:
2. Use child groups (sub groups) in Distributed Applications. To do this, create a new Parent Group and a new Child group in that parent group. (In the properties of parent group, you should specify the subgroups to add the child group). Then use that child group in Distributed Application. Alternatively, you can also create a new Parent group and add the group which you have used in the Distributed Application under subgroups so it becomes child group.
J.C. Hornbeck | Manageability Knowledge Engineer